java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.TemporalBroxOpticalFlow

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class TemporalBroxOpticalFlow
extends AlgorithmBase
```

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private double`	`alpha`
`private ModelImage`	`destuImage`
`private ModelImage`	`destvImage`
`private double`	`EPSILON`
`private double`	`gamma`
`private double`	`GAUSSIAN_SIGMA`
`private int`	`initer`
`private int`	`MAXITER`
`private int`	`nscales`
`private int`	`outiter`
`private double`	`PAR_DEFAULT_ALPHA`
`private double`	`PAR_DEFAULT_GAMMA`
`private int`	`PAR_DEFAULT_INNER_ITER`
`private int`	`PAR_DEFAULT_NSCALES`
`private int`	`PAR_DEFAULT_OUTER_ITER`
`private double`	`PAR_DEFAULT_TOL`
`private boolean`	`PAR_DEFAULT_VERBOSE`
`private double`	`PAR_DEFAULT_ZFACTOR`
`private double`	`SOR_PARAMETER`
`private double`	`TOL`
`(package private) TVL1FLOW`	`tvl1`
`private boolean`	`verbose`
`private double`	`zfactor`

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`TemporalBroxOpticalFlow()`
`TemporalBroxOpticalFlow(ModelImage destuImg, ModelImage destvImg, ModelImage srcImg, double alpha, double gamma, int nscales, double zfactor, double TOL, int inner_iter, int outer_iter, boolean verbose)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`brox_optic_flow(double[] I, double[] u, double[] v, int nx, int ny, int frames, double alpha, double gamma, double TOL, int inner_iter, int outer_iter, boolean verbose)`	Compute the optic flow with the Brox temporal method
`void`	`brox_optic_flow(double[] I, double[] u, double[] v, int nxx, int nyy, int frames, double alpha, double gamma, int nscales, double nu, double TOL, int inner_iter, int outer_iter, boolean verbose)`	Multiscale approach for computing the optical flow
`void`	`divergence_u(double[] u, double[] v, double[] psi1, double[] psi2, double[] psi3, double[] psi4, double[] psi5, double[] psi6, double[] div_u, double[] div_v, int nx, int ny, int nz)`	Compute the divergence of the optical flow
`void`	`Dxx(double[] I, double[] Ixx, int nx, int ny)`	Compute the second order X derivative
`void`	`Dxy(double[] I, double[] Ixy, int nx, int ny)`	Compute the second order XY derivative
`void`	`Dyy(double[] I, double[] Iyy, int nx, int ny)`	Compute the second order Y derivative
`void`	`gaussian(double[] in, double[] out, int xdim, int ydim, double sigma, int bc, int precision)`	Convolution with a Gaussian
`void`	`gaussian(double[] I, int xdim, int ydim, double sigma, int bc, int precision)`	Convolution with a Gaussian
`void`	`getminmax(double[] min, double[] max, double[] x, int n)`	Compute the max and min of an array
`void`	`gradient(double[] input, double[] dx, double[] dy, int nx, int ny)`	Compute the gradient with central differences
`void`	`gradient3(double[] input, double[] dx, double[] dy, double[] dz, int nx, int ny, int nz)`	Compute the 3D gradient with central differences
`void`	`image_normalization(double[] I, double[] In, int size)`	Function to normalize the images between 0 and 255
`void`	`mask3x3(double[] input, double[] output, int nx, int ny, double[] mask)`	Function to apply a 3x3 mask to an image
`double`	`process_frame(double[] Au, double[] Av, double[] Du, double[] Dv, double[] D, double[] du, double[] dv, double alpha, double[] psi1, double[] psi2, double[] psi3, double[] psi4, double[] psi5, double[] psi6, int f, int nx, int ny, int df0, int df1)`	Procedure to compute the motion increment in one frame
`void`	`psi_data(double[] I1, double[] I2, double[] I2x, double[] I2y, double[] du, double[] dv, double[] psip, int size)`	Compute the coefficients of the robust functional (data term)
`void`	`psi_divergence(double[] psi, double[] psi1, double[] psi2, double[] psi3, double[] psi4, double[] psi5, double[] psi6, int nx, int ny, int nz)`	Compute the coefficients of the divergence term
`void`	`psi_gradient(double[] I1x, double[] I1y, double[] I2x, double[] I2y, double[] I2xx, double[] I2xy, double[] I2yy, double[] du, double[] dv, double[] psip, int size)`	Compute the coefficients of the robust functional (gradient term)
`void`	`psi_smooth(double[] ux, double[] uy, double[] ut, double[] vx, double[] vy, double[] vt, double[] psi, int size)`	Compute the coefficients of the robust functional (smoothness term)
`void`	`runAlgorithm()`	Actually runs the algorithm.
`double`	`sor_iteration(double[] Au, double[] Av, double[] Du, double[] Dv, double[] D, double[] du, double[] dv, double alpha, double[] psi1, double[] psi2, double[] psi3, double[] psi4, double[] psi5, double[] psi6, int f, int df0, int df1, int i, int ny, int dy0, int dy1, int j, int nx, int dx0, int dx1)`	SOR iteration in one position

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

tvl1
```
TVL1FLOW tvl1
```

EPSILON
```
private final double EPSILON
```
See Also:

Constant Field Values

MAXITER
```
private final int MAXITER
```
See Also:

Constant Field Values

SOR_PARAMETER
```
private final double SOR_PARAMETER
```
See Also:

Constant Field Values

GAUSSIAN_SIGMA
```
private final double GAUSSIAN_SIGMA
```
See Also:

Constant Field Values

PAR_DEFAULT_ALPHA
```
private final double PAR_DEFAULT_ALPHA
```
See Also:

Constant Field Values

PAR_DEFAULT_GAMMA
```
private final double PAR_DEFAULT_GAMMA
```
See Also:

Constant Field Values

PAR_DEFAULT_NSCALES
```
private final int PAR_DEFAULT_NSCALES
```
See Also:

Constant Field Values

PAR_DEFAULT_ZFACTOR
```
private final double PAR_DEFAULT_ZFACTOR
```
See Also:

Constant Field Values

PAR_DEFAULT_TOL
```
private final double PAR_DEFAULT_TOL
```
See Also:

Constant Field Values

PAR_DEFAULT_INNER_ITER
```
private final int PAR_DEFAULT_INNER_ITER
```
See Also:

Constant Field Values

PAR_DEFAULT_OUTER_ITER
```
private final int PAR_DEFAULT_OUTER_ITER
```
See Also:

Constant Field Values

PAR_DEFAULT_VERBOSE
```
private final boolean PAR_DEFAULT_VERBOSE
```
See Also:

Constant Field Values

destuImage
```
private ModelImage destuImage
```

destvImage
```
private ModelImage destvImage
```

alpha
```
private double alpha
```

gamma
```
private double gamma
```

nscales
```
private int nscales
```

zfactor
```
private double zfactor
```

TOL
```
private double TOL
```

initer
```
private int initer
```

outiter
```
private int outiter
```

verbose
```
private boolean verbose
```

Constructor Detail

TemporalBroxOpticalFlow
```
public TemporalBroxOpticalFlow()
```

TemporalBroxOpticalFlow

public TemporalBroxOpticalFlow(ModelImage destuImg,
                               ModelImage destvImg,
                               ModelImage srcImg,
                               double alpha,
                               double gamma,
                               int nscales,
                               double zfactor,
                               double TOL,
                               int inner_iter,
                               int outer_iter,
                               boolean verbose)

Method Detail

runAlgorithm
```
public void runAlgorithm()
```
Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

gaussian

public void gaussian(double[] I,
                     int xdim,
                     int ydim,
                     double sigma,
                     int bc,
                     int precision)

Convolution with a Gaussian

gaussian

public void gaussian(double[] in,
                     double[] out,
                     int xdim,
                     int ydim,
                     double sigma,
                     int bc,
                     int precision)

Convolution with a Gaussian

mask3x3

public void mask3x3(double[] input,
                    double[] output,
                    int nx,
                    int ny,
                    double[] mask)

Function to apply a 3x3 mask to an image

Dxx

public void Dxx(double[] I,
                double[] Ixx,
                int nx,
                int ny)

Compute the second order X derivative

Dyy

public void Dyy(double[] I,
                double[] Iyy,
                int nx,
                int ny)

Compute the second order Y derivative

Dxy

public void Dxy(double[] I,
                double[] Ixy,
                int nx,
                int ny)

Compute the second order XY derivative

gradient

public void gradient(double[] input,
                     double[] dx,
                     double[] dy,
                     int nx,
                     int ny)

Compute the gradient with central differences

gradient3

public void gradient3(double[] input,
                      double[] dx,
                      double[] dy,
                      double[] dz,
                      int nx,
                      int ny,
                      int nz)

Compute the 3D gradient with central differences

psi_divergence

public void psi_divergence(double[] psi,
                           double[] psi1,
                           double[] psi2,
                           double[] psi3,
                           double[] psi4,
                           double[] psi5,
                           double[] psi6,
                           int nx,
                           int ny,
                           int nz)

Compute the coefficients of the divergence term

divergence_u

public void divergence_u(double[] u,
                         double[] v,
                         double[] psi1,
                         double[] psi2,
                         double[] psi3,
                         double[] psi4,
                         double[] psi5,
                         double[] psi6,
                         double[] div_u,
                         double[] div_v,
                         int nx,
                         int ny,
                         int nz)

Compute the divergence of the optical flow

psi_data

public void psi_data(double[] I1,
                     double[] I2,
                     double[] I2x,
                     double[] I2y,
                     double[] du,
                     double[] dv,
                     double[] psip,
                     int size)

Compute the coefficients of the robust functional (data term)

psi_gradient

public void psi_gradient(double[] I1x,
                         double[] I1y,
                         double[] I2x,
                         double[] I2y,
                         double[] I2xx,
                         double[] I2xy,
                         double[] I2yy,
                         double[] du,
                         double[] dv,
                         double[] psip,
                         int size)

Compute the coefficients of the robust functional (gradient term)

psi_smooth

public void psi_smooth(double[] ux,
                       double[] uy,
                       double[] ut,
                       double[] vx,
                       double[] vy,
                       double[] vt,
                       double[] psi,
                       int size)

Compute the coefficients of the robust functional (smoothness term)

sor_iteration

public double sor_iteration(double[] Au,
                            double[] Av,
                            double[] Du,
                            double[] Dv,
                            double[] D,
                            double[] du,
                            double[] dv,
                            double alpha,
                            double[] psi1,
                            double[] psi2,
                            double[] psi3,
                            double[] psi4,
                            double[] psi5,
                            double[] psi6,
                            int f,
                            int df0,
                            int df1,
                            int i,
                            int ny,
                            int dy0,
                            int dy1,
                            int j,
                            int nx,
                            int dx0,
                            int dx1)

SOR iteration in one position

process_frame

public double process_frame(double[] Au,
                            double[] Av,
                            double[] Du,
                            double[] Dv,
                            double[] D,
                            double[] du,
                            double[] dv,
                            double alpha,
                            double[] psi1,
                            double[] psi2,
                            double[] psi3,
                            double[] psi4,
                            double[] psi5,
                            double[] psi6,
                            int f,
                            int nx,
                            int ny,
                            int df0,
                            int df1)

Procedure to compute the motion increment in one frame

brox_optic_flow

public void brox_optic_flow(double[] I,
                            double[] u,
                            double[] v,
                            int nx,
                            int ny,
                            int frames,
                            double alpha,
                            double gamma,
                            double TOL,
                            int inner_iter,
                            int outer_iter,
                            boolean verbose)

Compute the optic flow with the Brox temporal method

getminmax

public void getminmax(double[] min,
                      double[] max,
                      double[] x,
                      int n)

Compute the max and min of an array

image_normalization

public void image_normalization(double[] I,
                                double[] In,
                                int size)

Function to normalize the images between 0 and 255

brox_optic_flow

public void brox_optic_flow(double[] I,
                            double[] u,
                            double[] v,
                            int nxx,
                            int nyy,
                            int frames,
                            double alpha,
                            double gamma,
                            int nscales,
                            double nu,
                            double TOL,
                            int inner_iter,
                            int outer_iter,
                            boolean verbose)

Multiscale approach for computing the optical flow

Class TemporalBroxOpticalFlow

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

tvl1

EPSILON

MAXITER

SOR_PARAMETER

GAUSSIAN_SIGMA

PAR_DEFAULT_ALPHA

PAR_DEFAULT_GAMMA

PAR_DEFAULT_NSCALES

PAR_DEFAULT_ZFACTOR

PAR_DEFAULT_TOL

PAR_DEFAULT_INNER_ITER

PAR_DEFAULT_OUTER_ITER

PAR_DEFAULT_VERBOSE

destuImage

destvImage

alpha

gamma

nscales

zfactor

TOL

initer

outiter

verbose

Constructor Detail

TemporalBroxOpticalFlow

TemporalBroxOpticalFlow

Method Detail

runAlgorithm

gaussian

gaussian

mask3x3

Dxx

Dyy

Dxy

gradient

gradient3

psi_divergence

divergence_u

psi_data

psi_gradient

psi_smooth

sor_iteration

process_frame

brox_optic_flow

getminmax

image_normalization

brox_optic_flow